Alternatives and similar repositories for openproblems

Users that are interested in openproblems are comparing it to the libraries listed below

• theislab / scib
  Benchmarking analysis of data integration tools
  ☆374Updated 7 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆382Updated last month
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆375Updated 7 months ago
• scverse / pertpy
  Single-cell perturbation analysis
  ☆198Updated last week
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆214Updated 2 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆393Updated 4 months ago
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆467Updated last week
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆373Updated 2 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆220Updated this week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆227Updated last month
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆398Updated 3 weeks ago
• gao-lab / GLUE
  Graph-linked unified embedding for single-cell multi-omics data integration
  ☆423Updated 3 weeks ago
• theislab / scgen
  Single cell perturbation prediction
  ☆315Updated 8 months ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆221Updated last week
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆162Updated 3 years ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆461Updated 6 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆426Updated 3 weeks ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆245Updated 2 weeks ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆364Updated last week
• KrishnaswamyLab / MAGIC
  MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …
  ☆369Updated 10 months ago
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆317Updated last month
• theislab / moscot
  Multi-omic single-cell optimal transport tools
  ☆171Updated this week
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆313Updated 6 months ago
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆224Updated last year
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆237Updated last week
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆173Updated last year
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆140Updated 6 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆422Updated 2 months ago
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆213Updated 2 years ago
• Murali-group / Beeline
  BEELINE: evaluation of algorithms for gene regulatory network inference
  ☆192Updated 2 months ago